A method and an apparatus for aligning substrates are provided to reduce a manufacturing error of a PCB by improving an aligning accuracy of the PCB(Printed Circuit Board). A substrate(20) is loaded on a working plate(10). An electric line and an alignment mark(25) are printed on the loaded substrate. The alignment mark is used as reference information for aligning printing positions of the electric lines. The alignment mark is printed at the same time when the electric lines are printed on the substrate. The electric lines and the alignment marks are printed on the substrate by using a predetermined program.
